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Started by upstream project "BIOFORMATS-test-repo" build number 185 originally caused by: Started by upstream project "Trigger" build number 207 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins18167762485129346732.sh + '[' flex = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_29229_merge_ci -v /uod/idr/repos/curated/flex:/data -v /uod/idr-scratch/merge-ci/curated/flex:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 15:36:25,304 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 15:36:25,306 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 15:36:25,306 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:36:25,307 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:36:25,307 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 15:36:25,307 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 15:36:25,308 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 15:36:25,308 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:36:25,308 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:36:25,309 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 15:36:25,309 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 15:36:25,309 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 15:36:25,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 15:36:25,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 15:36:25,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 15:36:25,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 15:36:25,511 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 15:36:25,512 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 15:36:25,512 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 15:36:25,512 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 15:36:25,512 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 15:36:25,513 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 15:36:25,513 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 205 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-11 15:36:25,523] [main] java.version = 17.0.2 [testng] 15:36:25,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 15:36:25,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:36:25,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-11_15-36-25.log] [testng] 15:36:25,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-09-11 15:36:25,572] [main] testng.directory = /data [testng] [2024-09-11 15:36:25,573] [main] testng.configDirectory = /config [testng] [2024-09-11 15:36:25,581] [main] testng.multiplier = 1.0 [testng] [2024-09-11 15:36:25,582] [main] testng.in-memory = false [testng] [2024-09-11 15:36:25,583] [main] testng.allow-missing = false [testng] [2024-09-11 15:36:25,583] [main] user.language = en [testng] [2024-09-11 15:36:25,583] [main] user.country = ${user.country} [testng] [2024-09-11 15:36:25,583] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-11 15:36:40,316] [main] ---------------------------------------- [testng] [2024-09-11 15:36:40,316] [main] Total files: 791 [testng] [2024-09-11 15:36:40,317] [main] Scan time: 14.733 s (18 ms/file) [testng] [2024-09-11 15:36:40,317] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-11 15:40:05,805] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 15:40:05,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 15:40:05,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:05,807 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-11_15-40-05.log] [testng] 15:40:05,807 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9ee7e34 - End of configuration. [testng] [2024-09-11 15:40:05,940] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] 15:40:05,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 15:40:05,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:05,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-11_15-40-05.log] [testng] 15:40:05,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@780a43ec - End of configuration. [testng] [2024-09-11 15:40:06,015] [pool-1-thread-11] Initializing /data/tony/test.tiff: [testng] 15:40:06,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 15:40:06,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:06,016 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-11_15-40-06.log] [testng] 15:40:06,017 |-INFO in ch.qos.logback.core.sift.SiftProcessor@489be54f - End of configuration. [testng] [2024-09-11 15:40:06,131] [pool-1-thread-10] Initializing /data/tony/003008000.flex: [testng] 15:40:06,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 15:40:06,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:06,132 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-11_15-40-06.log] [testng] 15:40:06,132 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74d0f717 - End of configuration. [testng] [2024-09-11 15:40:06,194] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] 15:40:06,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 15:40:06,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:06,195 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-11_15-40-06.log] [testng] 15:40:06,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6db48209 - End of configuration. [testng] [2024-09-11 15:40:06,269] [pool-1-thread-8] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 15:40:06,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 15:40:06,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:06,270 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-11_15-40-06.log] [testng] 15:40:06,271 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ae25506 - End of configuration. [testng] [2024-09-11 15:40:06,414] [pool-1-thread-7] Initializing /data/qa-18096/002002001.flex: [testng] 15:40:06,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 15:40:06,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:06,415 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-11_15-40-06.log] [testng] 15:40:06,415 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f82be93 - End of configuration. [testng] [2024-09-11 15:40:06,512] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 15:40:06,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 15:40:06,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:06,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-11_15-40-06.log] [testng] 15:40:06,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6477d1f3 - End of configuration. [testng] [2024-09-11 15:40:07,460] [pool-1-thread-5] Initializing /data/stephane/002007000.flex: [testng] 15:40:07,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 15:40:07,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:07,461 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-11_15-40-07.log] [testng] 15:40:07,462 |-INFO in ch.qos.logback.core.sift.SiftProcessor@692d5e0b - End of configuration. [testng] [2024-09-11 15:40:07,531] [pool-1-thread-4] Initializing /data/tony/015002000.tiff: [testng] 15:40:07,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 15:40:07,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:07,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-11_15-40-07.log] [testng] 15:40:07,533 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28afa215 - End of configuration. [testng] [2024-09-11 15:40:07,694] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex: [testng] 15:40:07,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 15:40:07,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:07,696 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-11_15-40-07.log] [testng] 15:40:07,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a284b4e - End of configuration. [testng] [2024-09-11 15:40:07,761] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 15:40:07,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 15:40:07,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:40:07,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-11_15-40-07.log] [testng] 15:40:07,762 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51bea189 - End of configuration. [testng] [2024-09-11 15:40:11,704] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-09-11 15:40:12,786] [pool-1-thread-7] Initializing /data/tamjid/006003000.flex: [testng] [2024-09-11 15:40:12,855] [pool-1-thread-8] Initializing /data/tamjid/006005000.flex: [testng] [2024-09-11 15:40:12,962] [pool-1-thread-11] Initializing /data/stephane/006013000.flex: [testng] [2024-09-11 15:40:13,065] [pool-1-thread-5] Initializing /data/manuel/003003001.flex: [testng] [2024-09-11 15:40:13,315] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-09-11 15:40:13,538] [pool-1-thread-12] Initializing /data/qa-2983/004007000.flex: [testng] [2024-09-11 15:40:13,697] [pool-1-thread-9] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-09-11 15:40:14,349] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-09-11 15:40:15,422] [pool-1-thread-10] Initializing /data/tony/003003000.tiff: [testng] [2024-09-11 15:40:16,334] [pool-1-thread-7] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-09-11 15:40:16,849] [pool-1-thread-8] Initializing /data/tony/001001000_objects.flex: [testng] [2024-09-11 15:40:17,736] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-09-11 15:40:18,340] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2024-09-11 15:40:18,497] [pool-1-thread-9] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-09-11 15:40:19,459] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-09-11 15:40:19,615] [pool-1-thread-8] Initializing /data/achim/003003000.flex: [testng] [2024-09-11 15:40:20,752] [pool-1-thread-5] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-09-11 15:40:21,972] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-09-11 15:40:22,653] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex: [testng] [2024-09-11 15:40:23,882] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-09-11 15:40:24,401] [pool-1-thread-8] Initializing /data/ghislain/test.flex: [testng] [2024-09-11 15:40:25,245] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-09-11 15:40:25,647] [pool-1-thread-11] Initializing /data/anatole/001004000.flex: [testng] [2024-09-11 15:40:25,957] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-09-11 15:40:27,432] [pool-1-thread-10] Initializing /data/tony/test1.flex: [testng] [2024-09-11 15:40:27,668] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2024-09-11 15:40:29,599] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex: [testng] [2024-09-11 15:40:29,941] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-09-11 15:40:32,565] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 6 minutes 12 seconds Finished: SUCCESS